circos_ideogram: Create the description of chromosome markings.
In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

circos_ideogram

R Documentation

Create the description of chromosome markings.

Description

This function writes ideogram files for circos.

Usage

circos_ideogram(
  name = "default",
  conf_dir = "circos/conf",
  band_url = NULL,
  fill = "yes",
  stroke_color = "black",
  show_bands = "yes",
  fill_bands = "yes",
  thickness = "20",
  stroke_thickness = "2",
  label_font = "condensedbold",
  spacing_default = "0",
  spacing_break = "0",
  fill_color = "black",
  radius = "0.85",
  radius_padding = "0.05",
  label_size = "36",
  band_stroke_thickness = "2"
)

Arguments

`name`	Name of the configuration file to which to add the ideogram.
`conf_dir`	Where does the configuration live?
`band_url`	Provide a url for making these imagemaps?
`fill`	Fill in the strokes?
`stroke_color`	What color?
`show_bands`	Show the bands for the ideogram?
`fill_bands`	and fill them in?
`thickness`	How thick to color the lines
`stroke_thickness`	How much of them to fill in
`label_font`	What font to use.
`spacing_default`	How much space between elements.
`spacing_break`	Space between breaks.
`fill_color`	What color to fill
`radius`	Where on the circle to put them
`radius_padding`	How much to pad between radii.
`label_size`	How large to make the labels in px.
`band_stroke_thickness`	How big to make the strokes!